X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LYZ1LYZ, 1OHQ
experimental modelPDB 1OHQ1LYZ, 1OHQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298300 mM sodium citrate, 16% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3246.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.07α = 90
b = 39.24β = 104.16
c = 100.18γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2697.1498.62.41.524456

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1LYZ, 1OHQ2.2697.1422746125298.120.19230.18930.24839RANDOM14.923
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.870.35-0.38-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.824
r_dihedral_angle_4_deg24.604
r_dihedral_angle_3_deg13.985
r_dihedral_angle_1_deg7.248
r_long_range_B_refined3.332
r_long_range_B_other3.325
r_scangle_other1.75
r_angle_refined_deg1.709
r_mcangle_it1.594
r_mcangle_other1.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.824
r_dihedral_angle_4_deg24.604
r_dihedral_angle_3_deg13.985
r_dihedral_angle_1_deg7.248
r_long_range_B_refined3.332
r_long_range_B_other3.325
r_scangle_other1.75
r_angle_refined_deg1.709
r_mcangle_it1.594
r_mcangle_other1.594
r_scbond_it1.159
r_scbond_other1.159
r_mcbond_it0.962
r_mcbond_other0.949
r_angle_other_deg0.906
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3576
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement